Move files from repo root into .config folder

.claude/CLAUDE.md

@@ -0,0 +1 @@
+@../AGENTS.md

.coderabbit.yaml

@@ -9,10 +9,10 @@ reviews:
       instructions: "Never express concerns about potential ruff rule violations, even those rules mentioned in other agent instructions; a pre-commit hook already runs a ruff check. Do not warn about unnecessary super().__init__() calls; pyright prefers those to be present. Do not warn about missing type hints; a pre-commit hook already checks for that."
     - path: "**/.copier-answers.yml"
       instructions: "Do not comment about the `_commit` value needing to be a clean release tag. A CI job will fail if that is not the case."
-    - path: ".copier-managed-files.json"
+    - path: ".config/.copier-managed-files.json"
       instructions: "This file is auto-generated by copier on every `copier copy` or `copier update`. Do not edit manually and do not request changes to its content."
   instructions: |
-    If any changed files are listed in .copier-managed-files.json, add a single summary comment
+    If any changed files are listed in .config/.copier-managed-files.json, add a single summary comment
     (not one per file) noting which files are template-managed and that the changes may warrant
     backporting. The manifest has a "templates" array — each entry has "src" (template URL),
     optional "parent_src" (its parent template, forming a chain), and "managed_files". If a file

pyrefly.mutmut.toml → .config/pyrefly.mutmut.toml

@@ -4,7 +4,8 @@
 use-ignore-files = false
 disable-project-excludes-heuristics = true
 python-platform = "linux"
-project-includes = ["mutants/src/**"]
+project-includes = ["../mutants/src/**"]
 project-excludes = [
-    "**/generated/**",
+    # paths are relative to this config file (in .config/), so prefix with ../ to anchor at the repo root
+    "../**/generated/**",
 ]

pyrefly.toml → .config/pyrefly.toml

@@ -1,19 +1,20 @@
 project-excludes = [
+    # paths are relative to this config file (in .config/), so prefix with ../ to anchor at the repo root
     # excludes managed by this repository
-    "**/template",
+    "../**/template",
 
     # excludes managed by template
-    "**/vendor_files",
-    "**/generated",
-    "**/copier_template_resources",
-    "**/.claude/plugins", # similar to vendor_files, but these are gitignored and can contain arbitrary code, so exclude from type checking but not mutation testing
+    "../**/vendor_files",
+    "../**/generated",
+    "../**/copier_template_resources",
+    "../**/.claude/plugins", # similar to vendor_files, but these are gitignored and can contain arbitrary code, so exclude from type checking but not mutation testing
 ]
 # without this explicit "project-includes" and "search-path", pyrefly struggles to understand the tests folder
 project-includes = [
-                    "src",
-                    "tests"
+                    "../src",
+                    "../tests"
                   ]
-search-path = ["."]
+search-path = [".."]
 disable-project-excludes-heuristics = true # with this being enabled by default, pyrefly things the src is excluded because it's an editable local install
 python-platform = "linux"
 infer-with-first-use = false # more similar to pyright. must define the empty list type when instantiated

.devcontainer/devcontainer.json

@@ -28,13 +28,13 @@
         "-AmazonWebServices.aws-toolkit-vscode", // the AWS CLI feature installs this automatically, but it's causing problems in VS Code
         // basic tooling
         // "eamodio.gitlens@15.5.1",
-        "coderabbit.coderabbit-vscode@0.20.4",
+        "coderabbit.coderabbit-vscode@0.20.7",
         "ms-vscode.live-server@0.5.2025051301",
         "MS-vsliveshare.vsliveshare@1.0.5905",
-        "anthropic.claude-code@2.1.197",
+        "anthropic.claude-code@2.1.205",
         // Python
         "ms-python.python@2026.5.2026052901",
-        "meta.pyrefly@1.1.1",
+        "meta.pyrefly@1.1.9001",
         "ms-vscode-remote.remote-containers@0.414.0",
         "charliermarsh.ruff@2026.56.0",
         // Misc file formats
@@ -57,7 +57,9 @@
         "python.terminal.activateEnvironment": false, // uv manages the environment
         "ruff.nativeServer": "on",
         // TODO: see if there's a way to specify different configurations for different folders
-        "ruff.configuration": "/workspaces/copier-base-template/ruff-non-src.toml", // use the non-src configuration since it's less restrictive and won't show false positives and underline things
+        "ruff.configuration": "/workspaces/copier-base-template/.config/ruff-non-src.toml", // use the non-src configuration since it's less restrictive and won't show false positives and underline things
+        "python.pyrefly.configPath": "/workspaces/copier-base-template/.config/pyrefly.toml",
+        "prettier.configPath": ".config/.prettierrc",
         "[jsonc][json]": {
           "editor.defaultFormatter": "esbenp.prettier-vscode",
           "editor.formatOnSave": true
@@ -68,5 +70,5 @@
   "initializeCommand": "sh .devcontainer/initialize-command.sh",
   "onCreateCommand": "sh .devcontainer/on-create-command.sh",
   "postStartCommand": "sh .devcontainer/post-start-command.sh"
-  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): f239a981 # spellchecker:disable-line
+  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): 007af1ff # spellchecker:disable-line
 }

CONTRIBUTING.md → .github/CONTRIBUTING.md

@@ -27,7 +27,7 @@ By participating in this project, you agree to abide by our [Code of Conduct](./
 1. **Fork the repository** on GitHub.
 
 2. **Set up the Dev Container (Recommended Method)**
-   - Create a GitHub Codespace (`Code`->`Codespaces` in the GitHub web console of your cloned repository) OR click on the "Open in Devcontainer" link in the [Readme](./README.md)
+   - Create a GitHub Codespace (`Code`->`Codespaces` in the GitHub web console of your cloned repository) OR click on the "Open in Devcontainer" link in the [Readme](../README.md)
 
 3. **Make Your Changes**
    - Create a branch for your feature or bug fix:
@@ -107,7 +107,7 @@ We love hearing new ideas! If you have an idea for a feature:
 
 ## 📜 License
 
-By contributing, you agree that your contributions will be licensed under the same license as the project: [LICENSE](./LICENSE).
+By contributing, you agree that your contributions will be licensed under the same license as the project: [LICENSE](../LICENSE).
 
 ---
 

.github/workflows/ci.yaml

@@ -153,7 +153,7 @@ jobs:
 
       - name: Confirm instantiated template has copier answers file
         run: |
-          if [ ! -f "./new-template/.copier-answers.yml" ]; then
+          if [ ! -f "./new-template/.config/.copier-answers.yml" ]; then
             echo "Copier answers file not found in instantiated template location"
             exit 1
           fi
@@ -167,6 +167,7 @@ jobs:
           rm -rf .github # apparently this folder doesn't get removed with the previous command for some reason
           rm -rf .devcontainer # apparently this folder doesn't get removed with the previous command for some reason
           rm -rf .claude # apparently this folder doesn't get removed with the previous command for some reason
+          rm -rf .config # apparently this folder doesn't get removed with the previous command for some reason
           ls -la
       - name: Move the instantiated template into the repo root
         run: |

.pre-commit-config.yaml

@@ -45,6 +45,7 @@ repos:
     rev: 359573a3ff38f71c93e160f2ace96d118f6ff42e  # frozen: v1
     hooks:
       - id: typos
+        args: [--write-changes, --force-exclude, --config, .config/_typos.toml]
         exclude: |
           (?x)^(
               .*\.min.js|
@@ -108,6 +109,7 @@ repos:
     rev: 515f543f5718ebfd6ce22e16708bb32c68ff96e1  # frozen: v3.8.3
     hooks:
       - id: prettier
+        args: [--config, .config/.prettierrc]
         # TODO: get template YAML and MD files more in line with prettier expectations so we can start using prettier on those too
         exclude: |
           (?x)^(
@@ -234,7 +236,7 @@ repos:
     hooks:
       - id: ruff
         name: ruff-src
-        args: [--fix, --config=./ruff.toml]
+        args: [--fix, --config=./.config/ruff.toml]
         files: src/.+\.py$
         exclude: |
           (?x)^(
@@ -244,7 +246,7 @@ repos:
           )$
       - id: ruff
         name: ruff-non-src # tests, scripts and other non-source code
-        args: [--fix, --config=./ruff-non-src.toml]
+        args: [--fix, --config=./.config/ruff-non-src.toml]
         files: ^(?!src/)(?!.+/src/).+\.py$
         exclude: |
           (?x)^(
@@ -253,6 +255,7 @@ repos:
               template/.*|
           )$
       - id: ruff-format
+        args: [--config=./.config/ruff.toml]
         exclude: |
           (?x)^(
               .*/generated/graphql/.*|
@@ -272,7 +275,7 @@ repos:
               template/.*|
           )$
         args:
-          - --rcfile=./pylintrc.toml
+          - --rcfile=./.config/pylintrc.toml
         verbose: true
 
   - repo: local
@@ -299,7 +302,7 @@ repos:
     hooks:
       - id: pyrefly
         name: pyrefly
-        entry: bash -c "uv run pyrefly check"
+        entry: bash -c "uv run pyrefly check -c ./.config/pyrefly.toml"
         files: '.+\.py$'
         exclude: |
           (?x)^(

AGENTS.md

@@ -170,7 +170,7 @@ For more details, see README.md and docs/QUICKSTART.md.
 
 # Copier-Managed Files
 
-Files generated from upstream copier templates are listed in `.copier-managed-files.json` (if present).
+Files generated from upstream copier templates are listed in `.config/.copier-managed-files.json` (if present).
 The manifest has a `templates` array — one entry per template in the chain. Each entry has `src` (the template URL),
 `managed_files` (files it placed), and optionally `parent_src` (the template that generated it, forming the chain).
 

copier.yaml

@@ -86,7 +86,7 @@ template_publishes_releases:
 copier_answers_directory:
     type: str
     help: What directory within the instantiated template contains the .copier-answers.yml file? Use '.' for the root, or a subdirectory path (e.g. 'frontend').
-    default: "."
+    default: ".config"
 
 _tasks:
   - command: |
@@ -115,13 +115,13 @@ _tasks:
             fi
         done
   - command: |
-        if [ -f ruff.toml ]; then
+        if [ -f .config/ruff.toml ]; then
             echo "Updating ruff target-version from python_version..."
             py_major_minor="$(printf '%s' '{{ python_version }}' | cut -d. -f1,2)"
             py_tag="py$(printf '%s' "$py_major_minor" | tr -d '.')"
-            sed -i -E 's/^target-version = "py[0-9]+"/target-version = "'"$py_tag"'"/' ruff.toml
+            sed -i -E 's/^target-version = "py[0-9]+"/target-version = "'"$py_tag"'"/' .config/ruff.toml
         else
-            echo "ruff.toml not found; skipping Ruff target-version update."
+            echo ".config/ruff.toml not found; skipping Ruff target-version update."
         fi
   - command: |
         python3 '{{ _copier_conf.src_path }}/src/copier_base_template/copier_tasks/copier_provenance.py' \
@@ -131,6 +131,8 @@ _tasks:
 
 _min_copier_version: "9.8"
 
+_answers_file: ".config/.copier-answers.yml"
+
 _subdirectory: template
 
 _templates_suffix: .jinja-base

extensions/context.py

@@ -45,9 +45,10 @@ def hook(  # noqa: PLR0915 # yes, this is a lot of statements, but it's all just
         context["strawberry_graphql_version"] = (
             "==0.298.0"  # problems with strawberry pydantic in later versions...lost the context for exactly why...it was figured out a while ago, but has to do with being able to override resolvers and have the schema still keep the desired nullability
         )
-        context["fastapi_version"] = ">=0.138.2"
+        context["fastapi_version"] = ">=0.139.0"
         context["fastapi_offline_version"] = ">=1.7.7"
-        context["uvicorn_version"] = ">=0.49.0"
+        context["starlette_version"] = ">=1.3.1"
+        context["uvicorn_version"] = ">=0.51.0"
         context["lab_auto_pulumi_version"] = ">=0.2.3"
         context["ariadne_codegen_version"] = ">=0.18.0"
         context["pytest_mock_version"] = ">=3.15.1"
@@ -62,7 +63,7 @@ def hook(  # noqa: PLR0915 # yes, this is a lot of statements, but it's all just
         context["pytest_asyncio_version"] = ">=1.4.0"
         context["pytest_timeout_version"] = ">=2.4.0"
         context["pytest_reserial_version"] = ">=0.6.1"
-        context["python_faker_version"] = ">=40.23.0"
+        context["python_faker_version"] = ">=40.28.1"
         #######
         context["nuxt_ui_version"] = "^4.8.1"
         context["nuxt_version"] = "^4.4.6"

pyproject.toml

@@ -8,7 +8,7 @@ dependencies = [
     "pytest>=9.1.1",
     "pytest-cov>=7.1.0",
     "pytest-randomly>=4.1.0",
-    "faker>=40.23.0",
+    "faker>=40.28.1",
     "pyright[nodejs]>=1.1.411",
     "pyrefly>=1.1.1",
     "mutmut>=3.6.0",
@@ -41,7 +41,7 @@ do_not_mutate = [   "*/generated/*" , # do not mutate generated code, this is cr
 # mutants tree and excludes do_not_mutate files, so every reported type error falls inside a mutant
 # function and mutmut can attribute it. Without it, pyrefly checks the real source from the mutants/
 # cwd and reports errors on non-mutant lines, crashing with "Could not find mutant for type error".
-type_check_command = ['uv', 'run', 'pyrefly', 'check', '--output-format=json', '-c', '../pyrefly.mutmut.toml']
+type_check_command = ['uv', 'run', 'pyrefly', 'check', '--output-format=json', '-c', '../.config/pyrefly.mutmut.toml']
 do_not_mutate_patterns = [
     # disable mutations of all logger.info/debug/... statements
     'logger\.\w+',

pytest.ini

@@ -1,7 +1,7 @@
 [pytest]
 # Settings managed by the base template
 norecursedirs = node_modules .precommit_cache .npm_cache .pipenv_cache venv .venv .history
-addopts = --cov=src --cov-report html --cov-report term-missing:skip-covered --cov-config=./.coveragerc
+addopts = --cov=src --cov-report html --cov-report term-missing:skip-covered --cov-config=./.config/.coveragerc
 
 log_cli = 1
 log_cli_level = INFO

src/copier_base_template/copier_tasks/copier_provenance.py

@@ -49,9 +49,19 @@ class CommentFormat:
     ".node-version": CommentFormat("none", "none"),
 }
 
+_MANIFEST_RELPATH = Path(".config") / ".copier-managed-files.json"
+
+
+def _find_manifest(base_directory: Path) -> Path:
+    config_manifest = base_directory / _MANIFEST_RELPATH
+    if config_manifest.exists():
+        return config_manifest
+    return base_directory / ".copier-managed-files.json"
+
+
 _HEADER_BASE = """\
 ============== WARNING ==============================================================================
-File is managed by a copier template. See .copier-managed-files.json for details.
+File is managed by a copier template. See .config/.copier-managed-files.json for details.
 
 You are welcome to make changes to this file in your repo if they are custom to your project,
 but if the change should be shared with other projects, please backport it to the template repo.
@@ -65,7 +75,7 @@ def _build_header(template_src: str) -> str:
     lines: list[str] = list(_HEADER_BASE.split("\n"))
     # Replace the generic "File is managed" line with two lines: URL line + "See ..." line.
     lines[1] = f"File is managed by copier template: {template_src}"
-    lines.insert(2, "See .copier-managed-files.json for details.")
+    lines.insert(2, "See .config/.copier-managed-files.json for details.")
     return "\n".join(lines)
 
 
@@ -225,7 +235,10 @@ def apply_file_markers(
 
 
 def _read_parent_src(src_template_directory: Path) -> str | None:
-    answers_path = src_template_directory.parent / ".copier-answers.yml"
+    template_root = src_template_directory.parent
+    answers_path = template_root / ".config" / ".copier-answers.yml"
+    if not answers_path.exists():
+        answers_path = template_root / ".copier-answers.yml"
     if not answers_path.exists():
         return None
     text = answers_path.read_text(encoding="utf-8")
@@ -240,7 +253,8 @@ def update_manifest(
     managed_files: list[str],
     parent_src: str | None = None,
 ) -> None:
-    manifest_path = dst_directory / ".copier-managed-files.json"
+    manifest_path = dst_directory / _MANIFEST_RELPATH
+    manifest_path.parent.mkdir(parents=True, exist_ok=True)
 
     existing: dict[str, Any] = {}
     if manifest_path.exists():
@@ -269,13 +283,13 @@ def main() -> None:
     args = parser.parse_args()
 
     # header_src drives what URL appears in file headers (empty → generic "managed by a copier template" text).
-    # manifest_src is the key written to .copier-managed-files.json and is always non-empty.
+    # manifest_src is the key written to .config/.copier-managed-files.json and is always non-empty.
     header_src = args.template_src
     manifest_src = args.template_src or str(args.src_template_dir)
 
     ancestor_managed_by_src: dict[str, set[str]] = {}
     ancestor_parent_by_src: dict[str, str] = {}
-    ancestor_manifest_path = args.src_template_dir.parent / ".copier-managed-files.json"
+    ancestor_manifest_path = _find_manifest(args.src_template_dir.parent)
     if ancestor_manifest_path.exists():
         data: dict[str, Any] = json.loads(ancestor_manifest_path.read_text(encoding="utf-8"))
         # The ancestor manifest may contain paths with a "template/" prefix (from self-stamp

src/copier_base_template/openapi/openapi_schema_simplifier.py

@@ -3,6 +3,20 @@
 # This is unit tested in the https://github.com/LabAutomationAndScreening/copier-base-template repo. It is excluded from coverage checks in other repos, so be cautious about making changes downstream as opposed to the copier base template...really it's for parsing OpenAPI schema...so I can't think of a reason you'd need custom changes that are repo-specific that shouldn't be backported to the template
 
 
+def _merge_typed_members(typed_dicts: list[dict[str, JsonValue]]) -> dict[str, JsonValue] | None:
+    merged: dict[str, JsonValue] = {}
+    for typed_member in typed_dicts:
+        for key, value in typed_member.items():
+            if key == "type":
+                continue
+            if key not in merged:
+                merged[key] = value
+                continue
+            if merged[key] != value:
+                return None  # branches disagree on this key; a single merged schema would silently drop one value
+    return merged
+
+
 def _collapse_anyof(schema: dict[str, JsonValue]) -> None:
     any_of = schema.get("anyOf")
     if not isinstance(any_of, list):
@@ -24,9 +38,11 @@ def _collapse_anyof(schema: dict[str, JsonValue]) -> None:
             return  # enum/const apply to every type, so merging them would wrongly reject null and the sibling types
         typed_dicts.append(member)
         member_types.append(member_type)
+    merged = _merge_typed_members(typed_dicts)
+    if merged is None:
+        return  # branches carry conflicting per-key values; collapsing would be lossy, so leave the union as-is
     del schema["anyOf"]
-    for typed_member in typed_dicts:
-        schema.update({key: value for key, value in typed_member.items() if key != "type"})
+    schema.update(merged)
     schema["type"] = [*member_types, "null"]
 
 

template/.config/.coveragerc

@@ -0,0 +1 @@
+../../.config/.coveragerc

template/.config/.prettierrc

@@ -0,0 +1 @@
+../../.config/.prettierrc

template/.config/_typos.toml

@@ -0,0 +1 @@
+../../.config/_typos.toml

template/.config/pylintrc.toml

@@ -0,0 +1 @@
+../../.config/pylintrc.toml

template/.config/pyrefly.toml

@@ -0,0 +1 @@
+../../.config/pyrefly.toml